Alignments for a candidate for gatA in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Pseudomonas putida KT2440

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate PP_0931 PP_0931 Glutamyl-tRNA(Gln) amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Putida:PP_0931
          Length = 483

 Score =  494 bits (1272), Expect = e-144
 Identities = 245/480 (51%), Positives = 335/480 (69%), Gaps = 3/480 (0%)

Query: 6   HKIT--ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVD 63
           H++T  E+ + +  K     +L      RI+ +D ++ +F+++ E+ A   A+  D A  
Sbjct: 2   HQLTLAEIARGLADKSFSSEELTGALLARIKQLDPQINSFISVTEDLALGQARAAD-ARR 60

Query: 64  GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLN 123
              E   L G PI  KD   T G+RT+C SK+L+NF   YDATVV +L +A  VT+GK N
Sbjct: 61  AAGETSALLGAPIAHKDLFCTNGVRTSCGSKMLDNFKAPYDATVVAKLAEAGMVTLGKTN 120

Query: 124 MDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPA 183
           MDEFAMGS+ E+S Y   KNPWNL+ VPGGSSGGSAAAVAA  +P + G+DTGGSIRQPA
Sbjct: 121 MDEFAMGSANESSHYGAVKNPWNLEHVPGGSSGGSAAAVAARLLPATTGTDTGGSIRQPA 180

Query: 184 SFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANV 243
           +   + GLKPTYGRVSR+G++A+ASSLDQ GP+ RT ED A LLQ ++G D  DSTS   
Sbjct: 181 ALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCALLLQGMAGFDAKDSTSIEE 240

Query: 244 DVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSK 303
            VPD+ +SL   ++GL+I +PKEY G G+     + V A++K LE LGA  +E+SLP+ +
Sbjct: 241 PVPDYSASLNASLQGLRIGLPKEYFGAGLDPRIADLVQASVKELEKLGAVVKEISLPNMQ 300

Query: 304 YALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGT 363
           +A+  YY+++ +EAS+NL+RFDG+R+GYR +   +L DLYK++R EGFG EV+RRIM+GT
Sbjct: 301 HAIPAYYVIAPAEASSNLSRFDGVRFGYRCEEPKDLTDLYKRSRGEGFGVEVQRRIMVGT 360

Query: 364 FALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYA 423
           +ALS+GYYDAYY KAQ++R LIK DF   F   D+I+GPTTP PA+K+G  + DP+  Y 
Sbjct: 361 YALSAGYYDAYYVKAQQIRRLIKNDFMAAFNDVDLILGPTTPNPAWKLGAKSSDPVAAYL 420

Query: 424 NDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
            D+ TI  NLAG+PG+S+P G  DGLP+G+Q++  +F E  +  VAH ++Q TD H   P
Sbjct: 421 EDVYTITANLAGLPGLSMPAGFVDGLPVGVQLLAPYFQEGRLLNVAHRYQQVTDWHTRAP 480


Lambda     K      H
   0.315    0.134    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 558
Number of extensions: 14
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 485
Length of database: 483
Length adjustment: 34
Effective length of query: 451
Effective length of database: 449
Effective search space:   202499
Effective search space used:   202499
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate PP_0931 PP_0931 (Glutamyl-tRNA(Gln) amidotransferase subunit A)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00132.hmm
# target sequence database:        /tmp/gapView.24142.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.9e-180  585.5   0.0   4.4e-180  585.3   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0931  PP_0931 Glutamyl-tRNA(Gln) amido


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0931  PP_0931 Glutamyl-tRNA(Gln) amidotransferase subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.3   0.0  4.4e-180  4.4e-180       5     465 ..      13     474 ..       9     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 585.3 bits;  conditional E-value: 4.4e-180
                           TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiett 77 
                                         l +k++s++e++ ++l+ri++ + +in+f++vt++ al +a++ d++ a  e + l g pia Kd +++++++t+
  lcl|FitnessBrowser__Putida:PP_0931  13 LADKSFSSEELTGALLARIKQLDPQINSFISVTEDLALGQARAADARRAaGEtSALLGAPIAHKDLFCTNGVRTS 87 
                                         678899999************************************998876647********************* PP

                           TIGR00132  78 caSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaad 152
                                         c+Sk+L+n+++pydatVv +l eag++++GktN+DEFamGs+ e+S +g++knP+n e+vpGGSsgGsaaavaa 
  lcl|FitnessBrowser__Putida:PP_0931  88 CGSKMLDNFKAPYDATVVAKLAEAGMVTLGKTNMDEFAMGSANESSHYGAVKNPWNLEHVPGGSSGGSAAAVAAR 162
                                         *************************************************************************** PP

                           TIGR00132 153 lvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDsts 227
                                         l p + g+DTGgSiRqPA++++  GlKPtYG+vSR+G++ayasSldq G+la++ ed al+l+ ++g D+kDsts
  lcl|FitnessBrowser__Putida:PP_0931 163 LLPATTGTDTGGSIRQPAALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCALLLQGMAGFDAKDSTS 237
                                         *************************************************************************** PP

                           TIGR00132 228 levkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiisps 302
                                         +e +v+++  +l++ l+gl++g+ ke+++ +ld ++++ +++ +++le+lga ++e+slp+++ a+++Yy+i+p+
  lcl|FitnessBrowser__Putida:PP_0931 238 IEEPVPDYSASLNASLQGLRIGLPKEYFGAGLDPRIADLVQASVKELEKLGAVVKEISLPNMQHAIPAYYVIAPA 312
                                         *************************************************************************** PP

                           TIGR00132 303 EassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefe 377
                                         Eassnl+r+dg+r+G+r ee+k+l++ly+++R egfg ev+rRim+G+yals++yyd+yy kAq++r+li+++f 
  lcl|FitnessBrowser__Putida:PP_0931 313 EASSNLSRFDGVRFGYRCEEPKDLTDLYKRSRGEGFGVEVQRRIMVGTYALSAGYYDAYYVKAQQIRRLIKNDFM 387
                                         *************************************************************************** PP

                           TIGR00132 378 klfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkk 452
                                          +f++vD+i++pt+p  a klg+k +dp++ yl+Dv+t++anlaGlp++s+P+g   +glp+G+q+ + +f++ +
  lcl|FitnessBrowser__Putida:PP_0931 388 AAFNDVDLILGPTTPNPAWKLGAKSSDPVAAYLEDVYTITANLAGLPGLSMPAGFV-DGLPVGVQLLAPYFQEGR 461
                                         ********************************************************.7***************** PP

                           TIGR00132 453 llsvakaleqald 465
                                         ll+va+ ++q +d
  lcl|FitnessBrowser__Putida:PP_0931 462 LLNVAHRYQQVTD 474
                                         ********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (483 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.37
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis